HEADER HYDROLASE/DNA 06-MAY-12 4F1H TITLE CRYSTAL STRUCTURE OF TDP2 FROM DANIO RERIO COMPLEXED WITH A SINGLE TITLE 2 STRAND DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(P*TP*GP*CP*AP*G)-3'); COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 2; COMPND 7 CHAIN: A; COMPND 8 SYNONYM: TYR-DNA PHOSPHODIESTERASE 2, 5'-TYROSYL-DNA COMPND 9 PHOSPHODIESTERASE, 5'-TYR-DNA PHOSPHODIESTERASE, TRAF AND TNF COMPND 10 RECEPTOR-ASSOCIATED PROTEIN HOMOLOG; COMPND 11 EC: 3.1.4.-; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: TYROSYL-DNA PHOSPHODIESTERASE 2; COMPND 15 CHAIN: B; COMPND 16 SYNONYM: TYR-DNA PHOSPHODIESTERASE 2, 5'-TYROSYL-DNA COMPND 17 PHOSPHODIESTERASE, 5'-TYR-DNA PHOSPHODIESTERASE, TRAF AND TNF COMPND 18 RECEPTOR-ASSOCIATED PROTEIN HOMOLOG; COMPND 19 EC: 3.1.4.-; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 5 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 6 ORGANISM_TAXID: 7955; SOURCE 7 GENE: TDP2, TTRAP, TTRAPL, SI:CH211-81E5.5, SI:DKEY-218N20.5; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 MOL_ID: 3; SOURCE 11 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 12 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 13 ORGANISM_TAXID: 7955; SOURCE 14 GENE: TDP2, TTRAP, TTRAPL, SI:CH211-81E5.5, SI:DKEY-218N20.5; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 5'-TYROSYL DNA PHOSPHODIESTERASE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.SHI,K.KURAHASHI,H.AIHARA REVDAT 3 28-FEB-24 4F1H 1 REMARK LINK REVDAT 2 02-JAN-13 4F1H 1 JRNL REVDAT 1 31-OCT-12 4F1H 0 JRNL AUTH K.SHI,K.KURAHASHI,R.GAO,S.E.TSUTAKAWA,J.A.TAINER,Y.POMMIER, JRNL AUTH 2 H.AIHARA JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF 5'-PHOSPHOTYROSINE JRNL TITL 2 ADDUCTS BY TDP2. JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 1372 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 23104058 JRNL DOI 10.1038/NSMB.2423 REMARK 2 REMARK 2 RESOLUTION. 1.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 67729 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.950 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.8890 - 4.0040 1.00 5040 154 0.1549 0.1667 REMARK 3 2 4.0040 - 3.1783 1.00 4850 148 0.1412 0.1733 REMARK 3 3 3.1783 - 2.7766 1.00 4801 145 0.1658 0.1752 REMARK 3 4 2.7766 - 2.5228 1.00 4784 146 0.1612 0.2119 REMARK 3 5 2.5228 - 2.3420 1.00 4769 145 0.1640 0.2169 REMARK 3 6 2.3420 - 2.2039 1.00 4752 145 0.1632 0.2033 REMARK 3 7 2.2039 - 2.0935 1.00 4737 144 0.1575 0.1796 REMARK 3 8 2.0935 - 2.0024 1.00 4738 144 0.1616 0.1921 REMARK 3 9 2.0024 - 1.9253 1.00 4723 143 0.1650 0.1938 REMARK 3 10 1.9253 - 1.8589 1.00 4727 144 0.1711 0.2606 REMARK 3 11 1.8589 - 1.8007 1.00 4710 144 0.1948 0.2458 REMARK 3 12 1.8007 - 1.7493 1.00 4734 143 0.2126 0.2307 REMARK 3 13 1.7493 - 1.7032 0.99 4627 141 0.2583 0.2815 REMARK 3 14 1.7032 - 1.6617 0.80 3737 114 0.2957 0.2957 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.73 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 44.24 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.520 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.49020 REMARK 3 B22 (A**2) : 1.56280 REMARK 3 B33 (A**2) : -2.05310 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.014 4433 REMARK 3 ANGLE : 1.528 6041 REMARK 3 CHIRALITY : 0.116 664 REMARK 3 PLANARITY : 0.007 762 REMARK 3 DIHEDRAL : 14.949 1669 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 16.7302 -2.4536 -1.7162 REMARK 3 T TENSOR REMARK 3 T11: 0.1151 T22: 0.1180 REMARK 3 T33: 0.1145 T12: 0.0003 REMARK 3 T13: 0.0019 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.0786 L22: 0.1737 REMARK 3 L33: 0.0520 L12: -0.1186 REMARK 3 L13: -0.0418 L23: 0.0632 REMARK 3 S TENSOR REMARK 3 S11: -0.0173 S12: 0.0050 S13: -0.0091 REMARK 3 S21: 0.0113 S22: 0.0055 S23: 0.0111 REMARK 3 S31: 0.0300 S32: 0.0104 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4F1H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072335. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-11 REMARK 200 TEMPERATURE (KELVIN) : 96 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67804 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.660 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG AND SODIUM TARTRATE, PH 7, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 28.95900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.36600 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.55000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 52.36600 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.95900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.55000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O3' DG C 5 P PO4 C 101 1.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 DT C 1 P DT C 1 OP3 -0.111 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 DT C 1 OP1 - P - OP2 ANGL. DEV. = -15.3 DEGREES REMARK 500 DT C 1 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC C 3 O4' - C1' - N1 ANGL. DEV. = -5.3 DEGREES REMARK 500 DG C 5 C3' - C2' - C1' ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 275 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 153 57.34 35.85 REMARK 500 CYS A 239 139.29 96.35 REMARK 500 ARG A 303 -60.68 -93.39 REMARK 500 ARG A 323 74.87 -102.48 REMARK 500 ASP A 341 -67.64 -105.59 REMARK 500 MET A 348 46.98 -95.36 REMARK 500 THR B 153 57.26 35.38 REMARK 500 CYS B 239 145.94 87.64 REMARK 500 CYS B 239 144.15 87.70 REMARK 500 ALA B 277 -5.40 79.27 REMARK 500 ARG B 323 77.24 -100.39 REMARK 500 ASP B 341 -60.92 -105.12 REMARK 500 ASP B 341 -61.42 -105.12 REMARK 500 MET B 348 32.70 -92.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 PO4 C 101 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT C 1 OP1 REMARK 620 2 GLU A 161 OE2 105.0 REMARK 620 3 HOH A 531 O 80.6 82.1 REMARK 620 4 HOH A 678 O 85.4 151.3 73.1 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 C 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FPV RELATED DB: PDB REMARK 900 RELATED ID: 4F1I RELATED DB: PDB REMARK 900 RELATED ID: 4FVA RELATED DB: PDB REMARK 900 RELATED ID: 4GEW RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 A LARGE PORTION OF THE N-TERMINAL WAS NOT OBSERVED IN THE ELECTRON REMARK 999 DENSITY DBREF 4F1H A 120 369 UNP Q5XJA0 TYDP2_DANRE 120 369 DBREF 4F1H B 120 369 UNP Q5XJA0 TYDP2_DANRE 120 369 DBREF 4F1H C 1 5 PDB 4F1H 4F1H 1 5 SEQRES 1 C 5 DT DG DC DA DG SEQRES 1 A 250 ASP SER LYS LEU SER ILE ILE SER TRP ASN VAL ASP GLY SEQRES 2 A 250 LEU ASP THR LEU ASN LEU ALA ASP ARG ALA ARG GLY LEU SEQRES 3 A 250 CYS SER TYR LEU ALA LEU TYR THR PRO ASP VAL VAL PHE SEQRES 4 A 250 LEU GLN GLU LEU ILE PRO ALA TYR VAL GLN TYR LEU LYS SEQRES 5 A 250 LYS ARG ALA VAL SER TYR LEU PHE PHE GLU GLY SER ASP SEQRES 6 A 250 ASP GLY TYR PHE THR GLY ILE MET LEU ARG LYS SER ARG SEQRES 7 A 250 VAL LYS PHE LEU GLU SER GLU ILE ILE CYS PHE PRO THR SEQRES 8 A 250 THR GLN MET MET ARG ASN LEU LEU ILE ALA GLN VAL THR SEQRES 9 A 250 PHE SER GLY GLN LYS LEU TYR LEU MET THR SER HIS LEU SEQRES 10 A 250 GLU SER CYS LYS ASN GLN SER GLN GLU ARG THR LYS GLN SEQRES 11 A 250 LEU ARG VAL VAL LEU GLN LYS ILE LYS GLU ALA PRO GLU SEQRES 12 A 250 ASP ALA ILE VAL ILE PHE ALA GLY ASP THR ASN LEU ARG SEQRES 13 A 250 ASP ALA GLU VAL ALA ASN VAL GLY GLY LEU PRO ALA GLY SEQRES 14 A 250 VAL CYS ASP VAL TRP GLU GLN LEU GLY LYS GLN GLU HIS SEQRES 15 A 250 CYS ARG TYR THR TRP ASP THR LYS ALA ASN SER ASN LYS SEQRES 16 A 250 THR VAL PRO TYR VAL SER ARG CYS ARG PHE ASP ARG ILE SEQRES 17 A 250 PHE LEU ARG SER ALA LYS THR ALA PRO PRO VAL THR PRO SEQRES 18 A 250 ASP HIS MET ALA LEU ILE GLY MET GLU LYS LEU ASP CYS SEQRES 19 A 250 GLY ARG TYR THR SER ASP HIS TRP GLY ILE TYR CYS THR SEQRES 20 A 250 PHE ASN THR SEQRES 1 B 251 GLU ASP SER LYS LEU SER ILE ILE SER TRP ASN VAL ASP SEQRES 2 B 251 GLY LEU ASP THR LEU ASN LEU ALA ASP ARG ALA ARG GLY SEQRES 3 B 251 LEU CYS SER TYR LEU ALA LEU TYR THR PRO ASP VAL VAL SEQRES 4 B 251 PHE LEU GLN GLU LEU ILE PRO ALA TYR VAL GLN TYR LEU SEQRES 5 B 251 LYS LYS ARG ALA VAL SER TYR LEU PHE PHE GLU GLY SER SEQRES 6 B 251 ASP ASP GLY TYR PHE THR GLY ILE MET LEU ARG LYS SER SEQRES 7 B 251 ARG VAL LYS PHE LEU GLU SER GLU ILE ILE CYS PHE PRO SEQRES 8 B 251 THR THR GLN MET MET ARG ASN LEU LEU ILE ALA GLN VAL SEQRES 9 B 251 THR PHE SER GLY GLN LYS LEU TYR LEU MET THR SER HIS SEQRES 10 B 251 LEU GLU SER CYS LYS ASN GLN SER GLN GLU ARG THR LYS SEQRES 11 B 251 GLN LEU ARG VAL VAL LEU GLN LYS ILE LYS GLU ALA PRO SEQRES 12 B 251 GLU ASP ALA ILE VAL ILE PHE ALA GLY ASP THR ASN LEU SEQRES 13 B 251 ARG ASP ALA GLU VAL ALA ASN VAL GLY GLY LEU PRO ALA SEQRES 14 B 251 GLY VAL CYS ASP VAL TRP GLU GLN LEU GLY LYS GLN GLU SEQRES 15 B 251 HIS CYS ARG TYR THR TRP ASP THR LYS ALA ASN SER ASN SEQRES 16 B 251 LYS THR VAL PRO TYR VAL SER ARG CYS ARG PHE ASP ARG SEQRES 17 B 251 ILE PHE LEU ARG SER ALA LYS THR ALA PRO PRO VAL THR SEQRES 18 B 251 PRO ASP HIS MET ALA LEU ILE GLY MET GLU LYS LEU ASP SEQRES 19 B 251 CYS GLY ARG TYR THR SER ASP HIS TRP GLY ILE TYR CYS SEQRES 20 B 251 THR PHE ASN THR HET PO4 C 101 4 HET GOL A 401 6 HET MG A 402 1 HET GOL A 403 6 HET GOL B 401 6 HET GOL B 402 6 HETNAM PO4 PHOSPHATE ION HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 4 PO4 O4 P 3- FORMUL 5 GOL 4(C3 H8 O3) FORMUL 6 MG MG 2+ FORMUL 10 HOH *586(H2 O) HELIX 1 1 ASN A 137 THR A 153 1 17 HELIX 2 2 ILE A 163 ALA A 174 1 12 HELIX 3 3 CYS A 239 ASN A 241 5 3 HELIX 4 4 GLN A 242 ALA A 260 1 19 HELIX 5 5 ARG A 275 ASN A 281 1 7 HELIX 6 6 VAL A 292 LEU A 296 1 5 HELIX 7 7 GLN A 299 ARG A 303 5 5 HELIX 8 8 ASN B 137 THR B 153 1 17 HELIX 9 9 ILE B 163 ALA B 174 1 12 HELIX 10 10 CYS B 239 ASN B 241 5 3 HELIX 11 11 GLN B 242 ALA B 260 1 19 HELIX 12 12 VAL B 279 GLY B 283 5 5 HELIX 13 13 VAL B 292 LEU B 296 1 5 HELIX 14 14 GLN B 299 ARG B 303 5 5 SHEET 1 A 6 TYR A 177 GLU A 181 0 SHEET 2 A 6 PHE A 188 ARG A 194 -1 O LEU A 193 N LEU A 178 SHEET 3 A 6 VAL A 156 LEU A 162 -1 N VAL A 157 O MET A 192 SHEET 4 A 6 LEU A 123 ASN A 129 1 N ILE A 126 O PHE A 158 SHEET 5 A 6 GLY A 362 ASN A 368 -1 O ILE A 363 N SER A 127 SHEET 6 A 6 THR A 339 ILE A 346 -1 N THR A 339 O ASN A 368 SHEET 1 B 6 LYS A 199 CYS A 207 0 SHEET 2 B 6 ASN A 216 PHE A 224 -1 O GLN A 221 N GLU A 202 SHEET 3 B 6 GLN A 227 THR A 233 -1 O LEU A 231 N ALA A 220 SHEET 4 B 6 ALA A 264 ASP A 271 1 O ILE A 265 N TYR A 230 SHEET 5 B 6 ASP A 325 ARG A 330 -1 O PHE A 328 N PHE A 268 SHEET 6 B 6 VAL A 289 ASP A 291 -1 N CYS A 290 O LEU A 329 SHEET 1 C 2 TRP A 306 ASP A 307 0 SHEET 2 C 2 ARG A 321 CYS A 322 -1 O CYS A 322 N TRP A 306 SHEET 1 D 6 TYR B 177 GLU B 181 0 SHEET 2 D 6 PHE B 188 ARG B 194 -1 O LEU B 193 N LEU B 178 SHEET 3 D 6 VAL B 156 LEU B 162 -1 N LEU B 162 O PHE B 188 SHEET 4 D 6 LEU B 123 ASN B 129 1 N ILE B 126 O PHE B 158 SHEET 5 D 6 GLY B 362 PHE B 367 -1 O ILE B 363 N SER B 127 SHEET 6 D 6 PRO B 340 ILE B 346 -1 N ASP B 341 O THR B 366 SHEET 1 E 6 LYS B 199 CYS B 207 0 SHEET 2 E 6 ASN B 216 PHE B 224 -1 O GLN B 221 N GLU B 202 SHEET 3 E 6 GLN B 227 SER B 234 -1 O LEU B 231 N ALA B 220 SHEET 4 E 6 ALA B 264 ASP B 271 1 O ILE B 265 N TYR B 230 SHEET 5 E 6 ASP B 325 ARG B 330 -1 O ARG B 330 N VAL B 266 SHEET 6 E 6 VAL B 289 ASP B 291 -1 N CYS B 290 O LEU B 329 SHEET 1 F 2 TRP B 306 ASP B 307 0 SHEET 2 F 2 ARG B 321 CYS B 322 -1 O CYS B 322 N TRP B 306 LINK OP1 DT C 1 MG MG A 402 1555 1555 2.47 LINK OE2 GLU A 161 MG MG A 402 1555 1555 2.65 LINK MG MG A 402 O HOH A 531 1555 1555 2.81 LINK MG MG A 402 O HOH A 678 1555 1555 2.77 SITE 1 AC1 1 DG C 5 SITE 1 AC2 10 GLN A 299 HIS A 301 CYS A 302 HIS A 342 SITE 2 AC2 10 MET A 343 HOH A 517 HOH A 670 HOH A 762 SITE 3 AC2 10 HOH A 763 LEU B 178 SITE 1 AC3 4 GLU A 161 HOH A 531 HOH A 678 DT C 1 SITE 1 AC4 10 GLY A 186 TYR A 187 PHE A 200 LEU A 201 SITE 2 AC4 10 MET A 213 MET A 214 HOH A 505 HOH A 560 SITE 3 AC4 10 HOH A 598 HOH A 772 SITE 1 AC5 5 ARG B 303 ARG B 323 ARG B 326 HOH B 675 SITE 2 AC5 5 HOH B 782 SITE 1 AC6 3 LEU B 138 ALA B 165 TYR B 166 CRYST1 57.918 95.100 104.732 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017266 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010515 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009548 0.00000